壳斗科的壳斗系单源起源，来源于二歧聚伞花序（dichsia ）最外侧小枝，与其他类壳斗结构（cupule-like structure）不同。依据RPB2基因序列重建的系统关系支持壳斗多向演化的假说（F+1的规律，壳斗裂瓣数目比二歧聚伞花序中小花数目多1）。在各种壳斗类型中，具2果4裂瓣的水青冈类型保持了原始的性状，三棱栎型壳斗是较晚分化的类型，具有壳斗内裂瓣的金鳞果类型壳斗与其他类型壳斗有较近的共同祖先。
根据多种分子系统关系，结合形态性状分析，提出了壳斗科的新系统包括3个亚科：水青冈亚科Subfamily Fagoideae Oersted、三棱栎亚科Subfamily Trigonobalanoideae Lozano-C和栗亚科Subfamily Castaneoideae Oersted，2个族和7个属。
水青冈亚科包括水青冈属；三棱栎亚科包括广义三棱栎属；栗亚科包括金鳞果属、石栎属、栲属、栗属及栎属。按照传粉方式的不同，栗亚科分为2个族，虫媒的栗族Tribe Castaneae Schwarz和风媒的栎族Tribe Quercueae Schwarz，栗族包括金鳞果属、石栎属、栲属和栗属；栎族包括栎属。水青冈亚科和三棱栎亚科保留了较多原始性状，并处于多个分子系统中较基部的位置，属于低等壳斗类（the “lower” Fagaceae）；栗亚科具有更多的衍生性状，属于高等壳斗类（the “higher” Fagaceae）。
亚州东南部可能是壳斗科的次生演化中心，低等壳斗类在该区域的再次发展对形成高等壳斗类及其现代分布有重要影响 。低等壳斗类的现代分布区是北半球广布的祖先分布区收缩后的孑遗区（也有一定的扩张），而高等壳斗类的泛北极现代分布区可能是在亚洲东南部次生演化后再次扩散的结果。在地理分布特征上，祖先分布区广布是低等壳斗类的分布特征，而高等壳斗类则具有现代分布相对连续和广布的特征。; The RPB2 gene （codon the second largest subunit of RNA polymerase II） was used to reconstruct the phylogeny of the Fagaceae. The evolution of some morphological characters, and their biogeography patterns, are discussed, and a new taxonomic system of the Fagaceae is proposed. The main conclusions are summarized follows
1. RPB2 molecular phylogeny
A fragment of the RPB2 gene, a type of low copy nuclear gene that encodes the second largest subunit of RNA polymerase II, was used to investigate the phylogeny of the Fagaceae. The phylogeny of the RPB2 gene, based on sequences from exon 2 to exon11, indicated that the family Fagaceae was a monophyletic group and the family Nothofagaceae was not a sister group of it. In the Fagaceae, the genus Fagus is in the basal position, followed by the genus Trigonobalanus, a sister clad that includes the genera Chrysolepis, Castaneae, Castanopsis ,Lithocarpus and Quercus. The phylogeny of RPB2 suggested the genus Chrysolepis and shared a closer common ancestor with the the clade cortained genus Castaneae, and the genus Castanopsis and the genus Lithocarpus, but more evidence is needed to confirm this relationship. The RPB2 phylogeny was compatible with morphological characters evolution and with other molecular phylogenic hypotheses; therefore, it is a potentially valuable nuclear tool for phylogeny work in Fagaceae in the further.
2. The molecular evolution of RPB2 gene in Fagales
Ten exons (2nd to 11th) of the RPB2 gene (1271bp) were investigated. The degree of GC content variation was positively related with sequences changing in this region including introns. The base substitutions in exons 3, 5, 6, 7, 8 were higher than those in other exon regions. Changes in amino acids frequencies in RPB2 were coincident in 18 species. Compared with the outgroup, there were 28 amino acid substitutions, 14 of which occurred in the Fagales, distributed in exons 2, 3, 4, 5 and 8. This indicates that the RPB2 gene might be impacted by positive selection. Fourteen amino acid substitutions were located at the three-dimensional protein structure of intact RPB2 gene’ s product, 9 sites of which were located in the lower complex linker regions and 5 sites at the alpha- hylex and belta- sheet. These results provide important insights to the evolution of the Fagales using the three-dimensional structure of proteins.
3. Origion and evolution of cupule
The cupule is the most distinguishable character of the Fagaceae and has been the focus of much research. Many hypotheses have been proposed for the origin, evolution and morphological features of the cupule. These have been based on different types of evidence, but here we will use molecular phylogeny and fossil evidence.
Our results support the view that cupule valves originated from the outest branches of dichasium, and that cupules of the Fagaceae are diagnostic from other cupule-like organs with perianth origination in Fagales. There are three models of cupule evolution each characterized by distinct evolutionary tendencies, single, two and multi-directional respectively. Based on these models, we reconstructed the cupule’s evolution using the consensus of four recent molecular phylograms from different DNA fragments.
Our results indicate that cupules were monophyletic and that the Fagus cupule, with four cupule valves enclosing two triangular acorns, was the ancestral type, Trigonobalanopsis cupule was the inferior-ancestral type, and the Chrysolepis cupule which possesses inner valves, shared a common ancestor with other roundish cupules. Our conclusions are also unequivocal supported by fossil evidence, with affinity of extant homologous cupule. The consensus from the different molecular phylogeny hypotheses along with the age of fossil cupules that are similar to extant Fagaceae taxa, indicate that the cupule evolved in multi-directions, and that the small triangular narrow winged fruits surrounded by a dehiscent cupule was plesiomorphic, and that a bigger roundish fruit surrounded by an indehiscent cupule was synapomorphic. All those results provide the new evidence to explore evolution and phylogeny of Fagaceae.
4. Character evolution
The twenty-one trichomes characters were cladistic analysised and were mapped on the RPB2 phylogram. The results demonstrated 4 types of trichome evolution: the plesiomorphy, the synapomorphy, the diagnostic of genus, and the apomorphy with several origins. The trichome characters are more complex and diverse in derived lineages of the Fagaceae.
Oldest Fagaceae fossil (late Cretaceous, Santonian) supported anthophilous pollination was ancestral model, based on this, RPB2 molecular phylogeny interpreted that 2 origins of anemophilous pollination occurred in Fagaceae independently. Therefore, 2 kinds of pollination syndrome evolved in Fagaceae parallelly. Additionally, the evolution of other characters related with pollination strategy, such as flower structure, sex and axis of inflorescence and morphology of pollen grain probably be constrained by pollination syndrome.
5. New system of Fagaceae
Based on the molecular phylogenies and morphological analysis, a new taxonomic system of the family Fagaceae is proposed, that includes 3 subfamilies (Subfamily Fagoideae Oersted, Subfamily Trigonobalanoideae Lozano-C, and Subfamily Castaneoideae Oersted) and 2 tribes (Tribes Castaneae Schwarz, Tribes Quercueae Schwarz).The Subfamily Fagoideae includes the genus Fagus, and the Subfamily Trigonobalanoideae includes the genusTrigonobalanus s.l.. According to the pollination strategies, the Subfamily Castanoideae was divided into 2 tribes (tribes Castaneae Schwarz and Quercueae Schwarz). The Anthophilous tribe Castaneae includs the genus Chrysolepis, Lithocarpus, Castanea, and Castanopsis, and the anemophilous tribe Quercueae is composed of the genus Quercus.
Some diagnostic primary characters shared by the Subfamilies Fagoideae and Trigonobalanoide indicate that these 2 subfamilies are the “lower” Fagaceae. With more derived morphyology characters, Subfamily Castaneoideae is the “higher” Fagaceae. This new system is supported independently by the fossil records and the consensus of several molecular phylogenies from different DNA fragmants.
6. Biogeography study
The wide fossil distribution indicates that the ancestral area of the Fagaceae was a continuous Holactica area including temperate, subtropical and tropical Northern Hemisphere, formed at least before the Santonian during the Cretaceous though NALB, BLB or Malpighiaceae route. Before the early Paleocene, these continuous ancestral areas were separated by continental drift. Simultaneously, climate deterioratied from later Paleocene and the diversity of adaptations in the different groups have controlled the vicariance, dispersal and extinction of Fagaceae groups in all subareas.
A secondary origin center of the Fagaceae is proposed for Southeast Asia, for rich diversity of genus and species for 3 subfamilies, especially in advanced subfamily Castaneoideae. Possibly, the “higher” Fagaceae originated directly from the “lower” Fagaceae in Southeast Asia. The current disjunctive and narrow distributions of the“lower” Fagaceae were relics of wider ancestral distribution. However, the continuous and wider current distribution of the “higher” Fagaceae was the outcome of re-dispersal from secondary origination in Southeast Asia.|